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Old 05-11-2011, 05:04 AM   #1
wisosonic
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Location: Rouen-France

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Default BWA best combination of parameters

hi all

I am trying to align my illumina's reads using BWA to the human exome
and i am runnig it as defalut parameters ... so i am getting max of 45% of aligned reads ( without any filter on quality or depth )

does anyone have a good combination of parameters for BWA ?

thanks
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Old 05-11-2011, 06:25 PM   #2
2007lab
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Is your reads from whole genome or targeted sequencing?
I am also interested to know these, for SOLID, exome capture samples.
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